Study on Wusan Granule Anti-tumor Related Target Gene Screened by cDNA Microarray

Wusan Granule, the Ⅲ new drug, is composed of such traditional Chinese medicines as Radix Polygorri Multiflori Praeparata, Radix Noginseng and the like. In 2001, State Drug Administration of China approved clinical trial for Wusan Granule. Wusan Granule possesses the superiority of safety and effectiveness. Its main functions are to supplement Qi and nourish Yin, and to dissipate mass. The animal experiment showing the recipe for Wusan Granule can not only suppress Lewis lung carcinom…     

一种新型多类别生物芯片cDNA基因表达数据标准化方法

cDNA生物芯片表达数据广泛用于生物医学研究,利用计算机对其进行处理还有很多挑战性课题。该文提出了一种新的基于不变基因的多类生物芯片监督型集合cDNA表达数据标准化方法。在达到标准化的同时,该方法也可直接用于基因表达数据的特征选择,实验证明效果较好。     

双波长激光共聚焦生物芯片检测与图像处理

基于共聚焦检测原理,建立了双波长生物芯片检测系统。采用体全息滤光片,利用其反射衍射和带阻滤光特性,无需切换或改变光路,在同一光路中即可实现Cy3与Cy5荧光双波长扫描检测。提出了基于顺序形态变换的生物芯片荧光点阵图像的网格化处理方法,并对Cy3与Cy5荧光试剂点样玻片进行了扫描实验,对实验所得荧光点阵图像进行了网格化处理。实验结果显示,系统的检测灵敏度达到0.1 fluo/μm2,网格化算法简单、有效。     

双波长生物芯片荧光检测数据归一化方法研究

基于总值归一化法,通过顺序形态变换实现双色荧光图像数据的校正,对双通道检测的2种不同波长的Cy3、Cy5荧光图像进行了背景分析和归一化系数计算,数据分析显示双色荧光图像背景分割准确,依据其计算双色荧光校正信号,能消除检测通道(PMT)等因素造成的差异.该方法也适用于多波长荧光数据归一化.     

Cationic Polyelectrolyte Amplified Bead Array for DNA Detection with Zeptomole Sensitivity and Single Nucleotide Polymorphism Selectivity

A highly sensitive strand specific DNA assay, which consists of a peptide nucleic acid (PNA) probe, a cationic conjugated polymer ( PFVP ), and self‐assembled polystyrene beads in microwell arrays on silicon chip, is reported. PFVP , as an efficient signal amplifier and signal reporter, has been specially designed and synthesized to be compatible with commercial confocal microscopes for sensing on solid substrates. The assay operates on the net increase in negative charge at the PNA surface that occurs upon single‐stranded DNA hybridization, which subsequently allows complex formation with the positively charged PFVP to favor energy transfer between the polymer and Cy5‐labeled target. With maximized surface contact provided by bead arrays and signal amplification provided by PFVP , this assay allows detection of ～300 copies of Cy5‐labeled DNA using a commercial confocal microscope. In addition, the same strategy is also extended for label‐free DNA detection with a detection sensitivity of 150 attomole. Excellent discrimination against single nucleotide polymorphism (SNP) is also demonstrated for both Cy5‐labeled and label‐free target detection. This study indicates that cationic conjugated polymers have great potential to be incorporated into the widely used microarray technology for simplified process with improved detection sensitivity.     

Neural Network Normalization (N3) to Uncover the Differential Signal of cDNA Microarrays

cDNA microarray is a high throughput technology for gene expression analysis. Differing from conventional molecular approaches, which detect molecular targets on a one-by-one basis, cDNA microarray monitors gene expressions of living organisms on a global scale. However, the signal detected by a microarray assay contains a significant amount of noise. Certain types of noise are introduced by the systematic variations that are hardly avoidable by experimental approaches. Significant biological information can only be recognized after the original or raw data sets of microarray assay have been effectively processed. We report here our progress in establishing a Neural Network Normalization (N3) approach to cDNA microarray data processing. With the strong learning ability of the artificial neural network, the trained N3 algorithm is capable of the detection and suppression of systematic variations during microarray data processing and has plasticity in handling both linear and non-linear microarray data sets. The potential of this system in signal processing for other types of biochips, including nucleic acid and non-nucleic acid-based biochips, is yet to be explored.     

Signal processing techniques in genomic engineering

Now that the human genome has been sequenced, the measurement, processing, and analysis of specific genomic information in real time are gaining considerable interest because of their importance to better the understanding of the inherent genomic function, the early diagnosis of disease, and the discovery of new drugs. Traditional methods to process and analyze deoxyribonucleic acid (DNA) or ribonucleic acid data, based on the statistical or Fourier theories, are not robust enough and are time-consuming, and thus not well suited for future routine and rapid medical applications, particularly for emergency cases. In this paper, we present an overview of some recent applications of signal processing techniques for DNA structure prediction, detection, feature extraction, and classification of differentially expressed genes. Our emphasis is placed on the application of wavelet transform in DNA sequence analysis and on cellular neural networks in microarray image analysis, which can have a potentially large effect on the real-time realization of DNA analysis. Finally, some interesting areas for possible future research are summarized, which include a biomodel-based signal processing technique for genomic feature extraction and hybrid multidimensional approaches to process the dynamic genomic information in real time.     

Anatomy and Growth Characteristics of Conjugated Polyelectrolyte/DNA Aggregates

Conjugated polyelectrolytes (CPEs) have been widely used as light harvesting macromolecules to amplify the signals of fluorescent assays that betray the presence of various biomolecular targets. Electrostatic interactions play an important role in coordinating optical coupling events and lead to the formation of complexes between oppositely charged CPEs and the target species. Here, we combine for the first time optical studies and structural characterization by liquid phase atomic force microscopy (AFM) to provide a picture of aggregate structure and growth dynamics between cationic CPE and DNA as a function of charge ratio. Specifically, poly1 ₂₀ , a copolymer containing a backbone with 50% fluorene, 30% phenylene, and 20% 2,1,3‐benzothiadiazole (BT) units and pendant cationic groups was mixed with single stranded DNA (ssDNA) labeled with the Cy5 acceptor chromophore. Continuous addition of ssDNA‐Cy5 to poly1 ₂₀ leads to a saturation in Cy5 emission due to Cy5–Cy5 self‐quenching. Addition of ssDNA to a preformed poly1 ₂₀ /ssDNA‐Cy5 solution results in increased sensitization by energy transfer and a reduction of Cy5–Cy5 self quenching. Adsorption of aggregates onto negatively charged mica under water allows for direct imaging of the polyelectrolyte complexes as a function of charge ratio. The composite set of observations allows for the development of a model for aggregate growth, which is dynamic and ceases when the surface charge becomes sufficiently negative. This saturation point can be mitigated by addition of unlabeled ssDNA.     

Iterative normalization of cDNA microarray data

Describes an approach to normalizing microarray expression data. The novel feature is to unify the tasks of estimating normalization coefficients and identifying the control gene set. Unification is realized by constructing a window function over the scatter plot defining the subset of constantly expressed genes and by affecting optimization using an iterative procedure. The structure of window function gates contributions to the control gene set used to estimate normalization coefficients. This window measures the consistency of the matched neighborhoods in the scatter plot and provides a means of rejecting control gene outliers. The recovery of normalizational regression and control gene selection are interleaved and are realized by applying coupled operations to the mean square error function. In this way, the two processes bootstrap one another. We evaluate the technique on real microarray data from breast cancer cell lines and complement the experiment with a data cluster visualization study     

The effect of microarray image compression on expression-based classification

Current gene-expression microarrays carry enormous amounts of information. Compression is necessary for efficient distribution and storage. This paper examines JPEG2000 compression of cDNA microarray images and addresses the accuracy of classification and feature selection based on decompressed images. Among other options, we choose JPEG2000 because it is the latest international standard for image compression and offers lossy-to-lossless compression while achieving high lossless compression ratios on microarray images. The performance of JPEG2000 has been tested on three real data sets at different compression ratios, ranging from lossless to 45:1. The effects of JPEG2000 compression/decompression on differential expression detection and phenotype classification have been examined. There is less than a 4% change in differential detection at compression rates as high as 20:1, with detection accuracy suffering less than 2% for moderate to high intensity genes, and there is no significant effect on classification at rates as high as 35:1. The supplementary material is available at .     

An evolutionary approach for gene expression patterns

This study presents an evolutionary algorithm, called a heterogeneous selection genetic algorithm (HeSGA), for analyzing the patterns of gene expression on microarray data. Microarray technologies have provided the means to monitor the expression levels of a large number of genes simultaneously. Gene clustering and gene ordering are important in analyzing a large body of microarray expression data. The proposed method simultaneously solves gene clustering and gene-ordering problems by integrating global and local search mechanisms. Clustering and ordering information is used to identify functionally related genes and to infer genetic networks from immense microarray expression data. HeSGA was tested on eight test microarray datasets, ranging in size from 147 to 6221 genes. The experimental clustering and visual results indicate that HeSGA not only ordered genes smoothly but also grouped genes with similar gene expressions. Visualized results and a new scoring function that references predefined functional categories were employed to confirm the biological interpretations of results yielded using HeSGA and other methods. These results indicate that HeSGA has potential in analyzing gene expression patterns.     

一种高密度基因芯片设计的新方法

基因芯片是一种由高密度寡核苷酸探针所形成的微阵列.本文首先提出一种基因芯片上寡核苷酸探针设计的新思想,即变长变覆盖探针优化设计方法,通过该方法设计的寡核苷酸探针的杂交解链温度最大程度地保持一致,可有效地减少碱基杂交错配,提高基因芯片检测结果的可靠性.根据上述核心思想,本文提出具体的检测目标核酸序列及其突变的基因芯片设计方法.     

A novel Xenopus oocyte expression system based on cytoplasmic coinjection of T7-driven plasmids and purified T7-RNA polymerase.

The Xenopus laevis South African frog oocyte is a well suited and widely used system for protein biochemistry and functional studies. So far, two methods are commonly in use for the expression of exogenous proteins in this system. Investigators have the choice between cytoplasmic injections of in vitro synthesized cRNA or nuclear injections of cDNA. Here, we describe a new method for ion channel expression in oocytes, which consists of a coinjection of T7-driven cDNA and T7-RNA polymerase directly into the cytoplasm. This technique uses very limited amounts of purified enzyme and is also applicable to SP6 polymerase. Commercially available polymerases can also conveniently substitute for self-purified enzymes. The technique can be used for electrophysiological and biochemical analysis. In particular, high level expressions have been achieved for potassium (Shaker B, Kv1.2 and Kv1.3) and sodium (P mu 1.2) channels, and we also demonstrate efficient metabolic labeling of the calcium channel auxiliary beta 3 subunit. The properties of the channels expressed by this technique are indistinguishable from those of the channels expressed by classical methods. Expression of multi-subunit proteins was also achieved illustrating that the technique can be used for structure-function analyses. Moreover, this novel expression technique avoids many drawbacks of the two former techniques. It clearly bypasses the costly and time-consuming step of cRNA synthesis in vitro, prevents delicate cRNA manipulation and is easier to perform and more reliable than nuclear injection. Finally, it does not affect cell survival rate. These data indicate that the T7-RNA polymerase expression technique could be widely used in the future for the expression of exogenous proteins in the Xenopus oocyte system.     

Cluster analysis of gene expression data based on self-splitting and merging competitive learning

Cluster analysis of gene expression data from a cDNA microarray is useful for identifying biologically relevant groups of genes. However, finding the natural clusters in the data and estimating the correct number of clusters are still two largely unsolved problems. In this paper, we propose a new clustering framework that is able to address both these problems. By using the one-prototype-take-one-cluster (OPTOC) competitive learning paradigm, the proposed algorithm can find natural clusters in the input data, and the clustering solution is not sensitive to initialization. In order to estimate the number of distinct clusters in the data, we propose a cluster splitting and merging strategy. We have applied the new algorithm to simulated gene expression data for which the correct distribution of genes over clusters is known a priori. The results show that the proposed algorithm can find natural clusters and give the correct number of clusters. The algorithm has also been tested on real gene expression changes during yeast cell cycle, for which the fundamental patterns of gene expression and assignment of genes to clusters are well understood from numerous previous studies. Comparative studies with several clustering algorithms illustrate the effectiveness of our method.     

Galactose Encapsulated Multifunctional Nanoparticle for HepG2 Cell Internalization

The fluorescent dye Cy3 and galactose derivatives are covalently assembled with different ratios on the surfaces of magnetic nanoparticles (MNPs) to produce multifunctional HepG2 cancer cell–targeting agents and the effect of ligand spatial orientation on the MNP surface is investigated on targeting specificity. By using a mixture of bis‐N‐hydroxysuccinimide ester (a bifunctional linker) and OSu‐activated Cy3 (w/w = 30:1), stable and quantifiable fluorescent MNPs (Cy3@MNPs) are synthesized that could be subsequently loaded with galactosyl ligands. A mono‐antennary and two different tri‐antennary galactosyl ligands are individually immobilized on Cy3@MNPs, and the uptake efficiencies of the resulting galactosyl Cy3@MNPs by HepG2 and HeLa cells are investigated using confocal microscopy. The confocal images show that galactosyl Cy3@MNPs are sprayed over cytoplasm of the HepG2 cells, indicating that the MNP uptake occurs via receptor‐mediated endocytosis that is followed by release from endosomes. The results also reveal that the ligand spatial orientation affects the efficiency of the receptor‐mediated endocytosis and one of the tri‐antennary galactosyl ligands shows the best uptake efficiency owing to the optimal spatial presentation of the galactosyl moieties. Overall, it is shown that the MNP is a good ligand carrier and that, when pre‐assembled, the multivalent ligand structure enhances the interactions between the surface ligands of the MNPs and receptors of HepG2 cells. Additionally, the galactosyl Cy3@MNPs are not cytotoxic, indicating that they may potentially be used for in vivo applications.     

Controlled Sequential Assembly of DNA Nanoparticles Inside Cells Enabling Mitochondrial Interference

Developing artificial material systems to rationally interfere with organelles is emerging as a promising route to regulate the behaviors and fate of cells, thus providing new therapeutic strategies. Herein, a DNA nanoparticles (DNPs)-based material system is reported, which achieves controlled sequential assembly inside cells, and realizes specific interference toward mitochondria. Two types of DNPs are synthesized via radical polymerization, followed with cascade hybridization chain reaction of hairpin DNA with Cyanine5 (Cy5) for mitochondrial targeting, and with complementary sequences for base pairing, respectively. DNPs with Cy5 (Cy5-DNPs) first entered cells to target mitochondria, and the other DNPs with complementary sequences entered cells after an interval to sequentially assemble with Cy5-DNPs into aggregates via base pairing. Mitochondrial interference is achieved, including increased reactive oxygen species, decreased membrane potential, abnormal elevation of Ca²⁺ level, decreased adenosine triphosphate, and attenuated cellular migration rate. In particular, by regulating the intervals of two types of DNPs entering cells, the mitochondrial interference degree is controllably modulated. This work achieves regulated organelles interference via the precise controlled self-assembly of DNA nanostructures inside cells, which is envisioned to have great potential in precision biomedicine.     

高纯细晶A12O3陶瓷金属化工艺研究

本文主要从金属化配方、涂膏方法、金属化层的厚度、金属化温度和镍层的厚度等工艺角度对高纯、细晶Al2O3陶瓷的封接性能进行研究和分析。其结果显示,采用高Mo含量的金属化膏剂、丝网印刷的涂膏方法、金属化层的厚度约为20pm、在1450℃下烧结,镍层的厚度5μm左右时,其平均抗拉强度可达143MPa,超出行业标准50％以上,其显微结构更加连贯、均匀、致密。     

面向直线顶管机的双屏视觉标靶标定方法与精度评价

针对双屏视觉标靶前、后感光成像屏位姿关系难以标定的问题,提出一种基于坐标点云的感光成像屏位姿标定方法。该方法分别将前、后感光成像屏划分为n行n列的网格阵列,通过全站仪测量感光成像屏上每个网格角点的空间三维坐标,并利用工业相机实时获取感光成像屏上每个网格角点的图像二维坐标,结合图像二维坐标和空间三维坐标获得2D-3D映射关系,从而得到坐标点云数据。根据三公共点坐标系转换算法将坐标点云数据中的三维坐标统一到标靶坐标系下,进而确定相机与前、后感光成像屏的位姿关系,再通过网格索引方法对前、后感光成像屏的位姿关系进行求解。为评价标靶位姿测量精度,设计了静态测量重复性精度评定实验和绝对测量精度评定实验。实验结果表明:该标定方法的坐标静态测量重复性精度为0.13 mm、绝对测量精度为0.93 mm;方位角静态测量重复性精度优于0.01°、绝对测量精度优于0.05°。因此,该标定方法可以实现两个空间平面位姿关系的精确标定,且具有操作简便、精度高等特点,可用于双屏视觉标靶的标定。     

舰载机起飞着舰的机动目标显示技术

在三维显示领域中,机动目标实时显示问题始终是研究的热点,为了进一步提高机动目标显示的效果,在保证画面分辨率的前提下,减少时延。针对于Unity3D引擎和Visual C+[KG-1.5mm]+6.0平台的实时通信问题,以舰载机起飞着舰的实际过程为背景,研究实现了舰载机的三维显示系统。重点讨论了Unity3D和Visual C+[KG-1.5mm]+6.0的通信连接方法,实现了发送数据包来驱动三维模型的过程,以此来实时显示舰载机飞行的状态信息。此外,文中又给出了系统的逼真三维实现效果图。该系统为将来三维显示技术在指挥控制系统中的应用提供了一种有效方法。     

Caffeic Acid-Deferoxamine Self-Polymerization Coating on Ti Implant Promotes Osteointegration by Synergetic Regulation of Multi-Pathways in ONFH Mechanism

Osteonecrosis of the femoral head (ONFH) is a common but sophisticated multifactorial disease. In this study, the genomic characteristics of ONFH from the sequencing is first analyzed. Excepting ischemia and inflammation, some of differentially expressed genes (DEGs) are connected with autophagy. So, they are taken as the breakthrough points to design an auto polymerization coating of caffeic acid with grafting deferoxamine (DFO) and strontium on Ti substrate. In vitro cells and in vivo immunofluorescence and immunohistochemical results prove that the modified Ti can upregulate the expression of HIF-1α in mesenchymal stem cells (MSCs) and human umbilical vein endothelial cells (HUVECs) by receptors of TGF-β and TNFR on cell membrane. Interestingly, in MSCs, the upregulated HIF-1α can promote autophagy to some extent by HIF-1α/BNIP2 pathway. Meanwhile, appropriate autophagy and HIF-1α can regulate MSCs proliferation and osteogenic differentiation by STAT3/Notch pathway. However, in HUVECs, although autophagy increases slightly, the upregulated HIF-1α prefers to increase its downstream target gene VEGF and accelerate angiogenesis by the pathway of HIF-1α/VEGF. The results of in vivo implantation show that the modified Ti substrate can effectively enhance the integration effect of the implant by osteogenesis and angiogenesis. More significantly, the modified Ti can retard the further deterioration of ONFH by regulation of key genes.